The FSB says in a statement that Rustam Muminov is a member of the Hizb ut-Tahrir, which advocates the establishment of Islamic rule through a caliphate.
It also accuses Muminov of participation in the armed Tajik opposition during that country's 1992-97 civil war.
The UN refugee agency (UNHCR), Human Rights Watch, and other rights groups have condemned his expulsion. The European Court of Human Rights had urged Russia not to repatriate him.
Initial reports said Muminov was deported on October 24.
But the FSB statement states he was expelled today and does not specify which country he was sent to.
The FSB claims Muminov "participated in military operations and punitive expeditions against supporters of the Tajik president [Imomali Rakhmonov] and took part in the smuggling of weapons, narcotics, and gold into Tajikistan from Afghanistan" in the early 1990s.
Muminov was arrested in Moscow on October 17, days after a Russian regional court had cleared him of terror charges brought against him by Uzbek authorities. Those allegations stemmed from violence in Andijon, in eastern Uzbekistan, in May 2005 that authorities have blamed on foreign-backed religious extremists.
Russia Says Expelled Uzbek Member Of Terrorist Group